Journal of Bacteriology最新文献

{"title":"The PDZ domain of EpsC is required for extracellular secretion of VesB by the Type II secretion system in <i>Vibrio cholerae</i>.","authors":"Austin Shannon, Tanya Johnson, Cameron S Roberts, Catherine T Chaton, Konstantin V Korotkov, Maria Sandkvist","doi":"10.1128/jb.00144-25","DOIUrl":"10.1128/jb.00144-25","url":null,"abstract":"<p><p>The Type II Secretion System (T2SS) of the Gram-negative pathogen <i>Vibrio cholerae</i> is considered a virulence factor primarily because it facilitates the secretion of cholera toxin upon arrival of this pathogen in the human intestinal lumen, resulting in the profuse watery diarrhea associated with infection. Results from transposon mutagenesis screens suggest that the <i>V. cholerae eps</i> genes that code for the T2SS are essential. The deletion of these genes impairs the secretion of the T2SS's nearly two dozen protein substrates, leading to the selection of suppressor mutations, extracytoplasmic stress, and poor growth of the mutant bacteria. Here, we explore the role of the C-terminal PDZ domain of the T2SS component EpsC, and why transposon insertions in <i>pdz</i> do not affect bacterial viability unlike insertions in most other <i>eps</i> genes. Our data show that the deletion of <i>pdz</i> does not affect the growth of <i>V. cholerae,</i> and we demonstrate via mass spectrometry that the serine protease VesB is the only known T2SS substrate fully reliant on PDZ for secretion. We confirm this finding with immuno- and enzyme assays and show that the immunoglobulin (Ig)-like fold of VesB contains PDZ-dependent secretion information that can be grafted onto β-lactamase, causing this normally periplasmic protein to be secreted in a PDZ-dependent manner. This work adds to a growing body of evidence about substrate selection by the T2SS and reinforces the view that the C-terminal domain of EpsC and its homologs are required for the secretion of only a subset of T2SS substrates within a given species.</p><p><strong>Importance: </strong>The T2SS is common in Gram-negative pathogens, facilitating the secretion of various toxins and enzymes; however, the mechanisms of substrate selection and secretion remain poorly understood. Here, we demonstrate that the C-terminal PDZ domain of the T2SS \"clamp\" protein EpsC is only required for secretion of VesB in <i>V. cholerae</i> and that VesB's Ig-fold contains PDZ-dependent secretion information that can be functionally grafted onto a non-secreted periplasmic protein.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0014425"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369372/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144626436","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative genomics of <i>Pseudomonas paraeruginosa</i>.","authors":"Maxime Déraspe, Lori L Burrows, Romé Voulhoux, Daniela Centrón, Jacques Corbeil, Paul H Roy","doi":"10.1128/jb.00149-25","DOIUrl":"10.1128/jb.00149-25","url":null,"abstract":"<p><p>The PA7-clade (or group 3) of <i>Pseudomonas aeruginosa</i> is now recognized as a distinct species, <i>Pseudomonas paraeruginosa</i>. We report here the genomic sequences of six new strains of <i>P. paraeruginosa</i>: Zw26 (the first complete genome of a cystic fibrosis isolate of <i>P. paraeruginosa</i>)<i>,</i> draft genomes of four burn and wound strains from Argentina very closely related to PA7, and of Pa5196, the strain in which arabinosylation of type IV pili was documented. We compared the genomes of 82 strains of <i>P. paraeruginosa</i> and confirmed that the species is divided into two sub-clades. Core genomes are very similar, while most differences are found in \"regions of genomic plasticity\" (RGPs). Several genomic deletions were identified, and most are common to the CR1 sub-clade that includes Zw26 and Pa5196. All strains lack the type 3 secretion system (T3SS) and instead use an alternative virulence strategy involving an exolysin, a characteristic shared with group 5 <i>P</i>. <i>aeruginosa</i>. All strains tend to be multiresistant like PA7, with a significant proportion of carbapenem-resistant strains, either <i>oprD</i> mutants or carrying carbapenemase genes. Although <i>P. paraeruginosa</i> is still relatively rare, it has a worldwide distribution. Its multiresistance and its alternative virulence strategy need to be considered in future therapeutic development.IMPORTANCE<i>Pseudomonas aeruginosa</i> is an important opportunistic pathogen causing respiratory infections, notably in cystic fibrosis, and burn and wound infections. Our study reports six new genomes of <i>Pseudomonas paraeruginosa</i>, a new species recently reported as distinct from <i>P. aeruginosa</i>. The number of sequenced genomes of <i>P. paraeruginosa</i> is only about 1% that of <i>P. aeruginosa</i>. We compare the genomic content of nearly all strains of <i>P. paraeruginosa</i> in GenBank, highlighting the differences in core and accessory genomes, antimicrobial resistance genes, and virulence factors. This novel species is very similar in environmental spectrum to <i>P. aeruginosa</i> but is notably resistant to last-line antibiotics and uses an alternative virulence strategy based on exolysin-this strategy being shared with some <i>P. aeruginosa</i> outliers.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0014925"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369383/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144707535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA methylation affects gene expression but not global chromatin structure in <i>Escherichia coli</i>.","authors":"Willow Jay Morgan, Haley M Amemiya, Lydia Freddolino","doi":"10.1128/jb.00540-24","DOIUrl":"10.1128/jb.00540-24","url":null,"abstract":"<p><p>The activity of DNA adenine methyltransferase (Dam) and DNA cytosine methyltransferase (Dcm) together account for nearly all methylated nucleotides in the <i>Escherichia coli</i> K-12 MG1655 genome. Previous studies have shown that perturbation of DNA methylation alters <i>E. coli</i> global gene expression, but it is unclear whether the methylation state of Dam or Dcm target sites regulates local transcription. In recent genome-wide experiments, we observed an underrepresentation of Dam sites in transcriptionally silent extended protein occupancy domains (EPODs), prompting us to hypothesize that EPOD formation is caused partially by low Dam site density. We thus hypothesized that a methylation-deficient version of MG1655 would show large-scale aberrations in chromatin structure. To test our hypothesis, we cloned methyltransferase deletion strains and performed global protein occupancy profiling using high-resolution <i>in vivo</i> protein occupancy display (IPOD-HR), chromatin immunoprecipitation for RNA polymerase (RNAP-ChIP), and transcriptome abundance profiling using RNA-seq. Our results indicate that loss of DNA methylation does not result in large-scale changes in genomic protein occupancy such as the formation of EPODs, indicating that the previously observed depletion of Dam sites in EPODs is correlative, rather than causal, in nature. However, loci with dense clustering of Dam methylation sites show methylation-dependent changes in local RNA polymerase and total protein occupancy, but local transcription is unaffected. Our transcriptome profiling data indicate that deletion of <i>dam</i> and/or <i>dcm</i> results in significant expression changes within some functional gene categories including SOS response, flagellar synthesis, and translation, but these expression changes appear to result from indirect regulatory consequences of methyltransferase deletion. In agreement with the downregulation of genes involved in flagellar synthesis, <i>dam</i> deletion is characterized by a swimming motility-deficient phenotype. We conclude that DNA methylation does not control the overall protein occupancy landscape of the <i>E. coli</i> genome and that observable changes in gene regulation generally do not result from the regulatory consequences of the local methylation states.IMPORTANCEPrevious studies of <i>E</i>. coli chromatin structure revealed a statistical association between the presence of silenced, highly protein-occupied regions of the genome and the depletion of modification sites for Dam methyltransferase. Here, we show that loss of DNA methylation does not substantively affect global chromatin structure in <i>E. coli</i>, thus demonstrating that the previously observed correlation was not causal. However, we observed specific methylation-dependent changes in gene expression, particularly affecting the SOS response, flagellar synthesis, and translation. These effects appear to be indirect regulatory consequences of methyltransfer","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0054024"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144626434","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell surface differences within the genus <i>Methanosarcina</i> shape interactions with the extracellular environment.","authors":"Amelia-Elena Rotaru, Ghazaleh Gharib, Abdalluh Jabaley, Konstantinos Anestis, Rhitu Kotoky","doi":"10.1128/jb.00112-25","DOIUrl":"10.1128/jb.00112-25","url":null,"abstract":"<p><p><i>Methanosarcina</i> are metabolically versatile methanogenic archaea that can perform extracellular electron transfer (EET), with important ecological and biotechnological implications. These archaea are broadly classified into two types (Type I and Type II) based on their energy metabolism and also differ in their aggregation-disaggregation behavior, cell surface properties, and electron transfer strategies. Type I <i>Methanosarcina</i> typically form large multicellular aggregates within a methanochondroitin extracellular matrix, thrive in organic-rich environments, play a key role in anaerobic digestion during wastewater treatment, and can perform EET. However, their mechanism of EET remains unresolved. In contrast, Type II <i>Methanosarcina</i> rely on multiheme c-type cytochromes for EET and are better adapted to low-organic, mineral-rich environments such as deep-sea sediments and aquifers, where they contribute to methane emissions. Despite their significance, the molecular mechanisms behind EET in <i>Methanosarcina</i>-particularly for Type I-remain poorly understood. This review highlights what is known and what is unknown regarding the surface biology of <i>Methanosarcina</i>, their EET strategies, and biogeochemical and industrial roles, emphasizing the need for further research to unlock their full potential in sustainable methane management.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0011225"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369344/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144707534","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DNA replication initiation timing is important for maintaining genome integrity.","authors":"Tristan T Reed, Abigail H Kendal, Katherine J Wozniak, Lyle A Simmons","doi":"10.1128/jb.00175-25","DOIUrl":"10.1128/jb.00175-25","url":null,"abstract":"<p><p>DNA replication is regulated by factors that promote or inhibit initiation. In <i>Bacillus subtilis,</i> YabA is a negative regulator of replication initiation, while the newly identified kinase CcrZ is a positive regulator. The consequences of under-initiation or over-initiation of replication on genome stability remain unclear. In this work, we measure the origin-to-terminus ratio as a proxy for replication initiation activity. We show that Δ<i>ccrZ</i> and several <i>ccrZ</i> alleles under-initiate DNA replication, while ablation of <i>yabA</i> or overproduction of CcrZ leads to over-initiation. We find that cells under-initiating DNA replication have few incidents of replication fork stress as determined by the low frequency formation of RecA-GFP foci compared with wild type. In contrast, cells over-initiating replication show levels of RecA-GFP foci formation analogous to cells directly challenged with DNA-damaging agents. We show that cells under-initiating and over-initiating DNA replication are both sensitive to mitomycin C, demonstrating that changes in replication initiation frequency cause an increase in sensitivity to genotoxic stress. With these results, we propose that cells under-initiating DNA replication are sensitive to DNA damage due to asynchronous DNA replication, leading to inefficient homologous recombination. In cells over-initiating replication, we propose that an increase in the number of replication forks leads to replication fork stress, which is further exacerbated by chromosomal DNA damage. Together, our study shows that DNA replication initiation frequency must be tightly controlled because changes in initiation influence replication fork fate and the capacity of cells to efficiently repair damage to their genetic material.IMPORTANCEThe regulation of DNA replication is fundamental to cell growth and cell cycle control. In eukaryotes, under-initiation or over-initiation leads to genome instability. In bacteria, it is unclear how changes in replication initiation frequency impact DNA replication status and genome integrity. We show that tight regulation of DNA replication initiation is critical for maintaining genome integrity. Cells over-initiating or under-initiating DNA replication are sensitive to DNA damage. Furthermore, cells over-initiating DNA replication experience replication fork stress at levels that phenocopy those observed in cells challenged with DNA damage from mitomycin C. Our results establish the critical importance of properly regulating DNA replication initiation frequency because an imbalance in initiation results in replication fork perturbations, deficiencies in DNA repair, and genome instability.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0017525"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369353/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144674887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic and biochemical analyses reveal direct interactions between LitR and genes important for <i>Vibrio fischeri</i> physiology, including biofilm production.","authors":"Brittany L Fung, Chase Mullins, Douglas B Rusch, Elizabeth G Musto, Julia C van Kessel, Karen L Visick","doi":"10.1128/jb.00042-25","DOIUrl":"10.1128/jb.00042-25","url":null,"abstract":"<p><p>Bacteria can link gene expression to population density to promote group behaviors using quorum sensing. Quorum sensing controls a multitude of bacterial processes, such as virulence, motility, and biofilm formation. In <i>Vibrio fischeri</i>, the quorum-sensing-dependent transcription factor LitR inhibits biofilm formation. A previous study showed that LitR inhibits transcription (~1.4-fold) of the <i>bcs</i> locus, which comprises the genes responsible for producing the cellulose polysaccharide. However, beyond that, the mechanism of LitR-mediated inhibition of biofilm formation was unknown. Here, we find that LitR transcriptionally activates <i>pdeV</i>, which encodes a c-di-GMP phosphodiesterase that indirectly promotes cleavage of the large adhesive protein LapV from the surface of <i>V. fischeri</i>, leading to biofilm dispersal. LitR also induces transcription of the gene for sensor kinase VF_A1016, which we determined to be important for biofilm inhibition. Like the loss of LitR, the loss of VF_A1016 increased <i>bcs</i> transcription (~1.6-fold). Through chromatin immunoprecipitation sequencing (ChIP-seq), we found that LitR directly binds to the <i>VF_A1016</i> and <i>pdeV</i> regulatory region. In total, we identified 147 LitR-binding sites in the genome and confirmed transcriptional control over a subset of these putative regulatory targets. Specifically, we determined that LitR induces transcription of the genes encoding the diguanylate cyclase VF_1200 and the glyoxylate shunt protein AceB and inhibits expression of the putative transcription factor TfoY. These data expand our understanding of LitR-mediated regulation of genes involved in biofilm formation and the physiology of <i>V. fischeri</i>.IMPORTANCEBacteria can coordinate their behaviors on a population level using quorum sensing, a process that results in altered gene regulation. In <i>Vibrio fischeri</i>, the quorum-sensing-regulated transcription factor LitR inhibits the formation of biofilms, communities of attached and protected bacteria, by diminishing the production of cellulose. Here, we determined that LitR controls additional known or putative biofilm factors. We also identified other possible targets of LitR regulation by high-throughput chromatin immunoprecipitation sequencing. This work furthers our understanding of the established connection between quorum sensing and biofilm formation in <i>V. fischeri</i> strain ES114. These findings also have the potential to translate to known pathways in other <i>Vibrios</i> where quorum sensing and biofilm production are linked.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0004225"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369385/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterizing the <i>Staphylococcus aureus</i> fatty acid degradation operon.","authors":"Cindy Menjivar, Zachary R DeMars, Richard E Wiemels, Ronan K Carroll, Jeffrey L Bose","doi":"10.1128/jb.00089-25","DOIUrl":"10.1128/jb.00089-25","url":null,"abstract":"<p><p><i>Staphylococcus aureus</i> can supplement its endogenous fatty acid synthesis pathway (FASII) with exogenous fatty acids it acquires from the environment through the fatty acid kinase (Fak) complex. Although <i>S. aureus</i> has been thought to not degrade fatty acids, it does possess a potential <i>fadXDEBA</i> locus that contains all the genes necessary for β-oxidation. Using mRNA analysis, we determined that the <i>fadXDEBA</i> operon can be found on one polycistronic mRNA. Moreover, we identified the <i>fadX</i> promoter and a putative binding site within this region that is consistent with negative regulation by the metabolism-responsive regulator, Carbon Catabolite Protein A (CcpA). Indeed, in the absence of glucose or CcpA, we saw the <i>fadXDEBA</i> operon was derepressed. <i>S. aureus</i> is annotated to lack the crotonase domain of FadB; however, new analysis indicates it is present. To test the functionality of the <i>S. aureus</i> FadB, we performed complementation assays with <i>E. coli fad</i> mutants using minimal media supplemented with single fatty acids. We were able to restore the growth of <i>E. coli fad</i> mutants when providing <i>safadBA</i> genes on a plasmid and demonstrate that the SaFadB crotonase domain is required for complementation. Together, these data demonstrate the SaFadBA proteins are functional within a well-characterized fatty acid degradation system, and the <i>S. aureus fadXDEBA</i> operon is under strong catabolite repression.</p><p><strong>Importance: </strong><i>Staphylococcus aureus</i> has long been thought to lack a functional fatty acid degradation (Fad) pathway based on limited studies. Pathway analysis suggested the <i>S. aureus</i> FadB protein lacks a crotonase domain, which is essential for Fad activity. This study demonstrates that <i>S. aureus</i> FadB possesses a crotonase domain that has eluded identification likely due to the orientation of its two enzymatic domains. In addition, we show that the Fad pathway is under strong catabolite repression under standard laboratory conditions, which may have also contributed to its lack of detected activity. A new model of fatty acid metabolism is emerging in <i>S. aureus</i> that changes the understanding of how this bacterium synthesizes and metabolizes fatty acids.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0008925"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369327/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144649568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Extracellular defense of bacteria against antimicrobial peptides.","authors":"Osmel Fleitas, Eria A Rebollar, Víctor H Bustamante","doi":"10.1128/jb.00166-25","DOIUrl":"10.1128/jb.00166-25","url":null,"abstract":"<p><p>Antimicrobial peptides (AMPs) are short chains of amino acids naturally produced by all kingdoms of life, which exhibit broad-spectrum activity against bacteria, fungi, and viruses and thus play a crucial defense role in organisms. Unlike conventional antibiotics, AMPs are less prone to induce bacterial resistance since they can act on multiple targets, mainly affecting cell membranes. Thus, AMPs are considered promising antibiotic agents for medical applications. However, bacteria have developed different mechanisms to resist the action of AMPs, which operate at the extracellular, surface, and intracellular levels. Extracellular defense against AMPs is mediated by an arsenal of molecules or cell-derived particles or structures that are secreted and constitute the bacterial releasome. The bacterial releasome-associated factors can sequester, degrade, or chemically modify AMPs, thus providing individual and collective bacterial defense against AMPs. This minireview describes how diverse and impressive the releasome mechanisms mediating AMPs resistance are as a first line of defense.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0016625"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369334/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144760134","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sequence variability of BamA and FadL candidate vaccinogens suggests divergent evolutionary paths of <i>Treponema pallidum</i> outer membrane proteins.","authors":"Everton B Bettin, Farhang Aghakhanian, Christopher M Hennelly, Wentao Chen, Timothy C Davenport, Simon T Hackl, Andre A Grassmann, Fabio Vargas-Cely, Sebastián Silva, Jonny A García-Luna, Lady G Ramirez, Yinbo Jiang, Ligang Yang, Heping Zheng, Bin Yang, Petra Pospíšilová, David Šmajs, Mitch M Matoga, Irving F Hoffman, Eduardo López-Medina, Kay Nieselt, M Anthony Moody, Arlene C Seña, Juan C Salazar, Jonathan B Parr, Melissa J Caimano, Kelly L Hawley, Justin D Radolf","doi":"10.1128/jb.00159-25","DOIUrl":"10.1128/jb.00159-25","url":null,"abstract":"<p><p>Knowledge of <i>Treponema pallidum</i> subspecies <i>pallidum</i> (<i>TPA</i>) outer membrane protein (OMP) sequence variability is essential for understanding spirochete proliferation within endemic populations as well as the design of a globally effective syphilis vaccine. Our group has identified extracellular loops (ECLs) of <i>TPA</i> BamA (TP0326) and members of the FadL family (TP0548, TP0856, TP0858, TP0859, and TP0865) as potential components of a multivalent vaccine cocktail. As part of a consortium to explore <i>TPA</i> strain diversity, we mapped the variability of BamA and FadL orthologs in 186 <i>TPA</i> strains from Malawi, China, and Colombia onto predicted 3D structures. The 186 genomes fell into eight subclades (five Nichols- and three SS14-lineage) with substantial geographic restriction. Single nucleotide variants accounted for the large majority of proteoforms, with variability notably higher within the Nichols-lineage strains. Most mutations were in regions of the proteins predicted to be extracellular and harboring B cell epitopes. We observed a striking difference in the degree of variability between the six OMPs, suggesting that these proteins are following divergent evolutionary paths. Concatenation of OMP sequences recapitulated the phylogenetic structure of the <i>TPA</i> strains, effectively segregating within clades and largely clustering by subclades. Finally, we noted that BamA and FadL candidate ECL vaccinogens, previously shown to elicit antibodies that kill treponemes during <i>in vitro</i> cultivation, are well conserved. Taken as a whole, our study establishes a structural-phylogenetic approach for analyzing the forces shaping the host-pathogen interface in syphilis within endemic populations while informing the selection of vaccine targets.IMPORTANCESyphilis remains a major global health concern, reinforcing the need for a safe and effective vaccine. Understanding the variability of <i>TPA</i> OMPs is essential for tracking pathogen evolution and informing vaccine design. Here, we analyzed the variability of six <i>TPA</i> OMPs in 186 strains from Malawi, China, and Colombia, identifying protein-specific evolutionary patterns. Most mutations were localized in extracellular regions and, notably, appeared to correlate with the phylogenetic structure of <i>TPA</i>. Despite OMP heterogeneity, several candidate vaccinogens remained highly conserved, reinforcing their potential as globally effective vaccine targets. Our study establishes a structural-phylogenetic framework for dissecting the forces shaping the host-spirochete interface within endemic populations and provides a foundation for designing a globally effective syphilis vaccine.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0015925"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369335/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144835176","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Artificial cellulose derivatives are metabolized by select human gut Bacteroidota upon priming with common plant β-glucans.","authors":"Deepesh Panwar, William A Stewart, Andrew Rodd, Harry Brumer","doi":"10.1128/jb.00198-25","DOIUrl":"10.1128/jb.00198-25","url":null,"abstract":"<p><p>Synthetic ethers of cellulose (β(1,4)-glucan) are widely used in the food and pharmaceutical industry as thickeners, gelling agents, emulsifiers, and stabilizers. Consequently, humans ingest significant amounts of artificial cellulose derivatives in diets containing processed foods and through oral drug formulations. In the present study, we examined the potential of mixed-linkage β-glucan (MLG) and xyloglucan (XyG) polysaccharide utilization loci of autochthonous human gut (gastrointestinal tract) Bacteroidota to enable metabolism of artificial cellulose derivatives, based on the commonality of their backbone linkages. Two representative <i>Bacteroides</i> and six representative <i>Segatella</i> (syn. <i>Prevotella</i>) strains all failed to grow on carboxymethyl cellulose (CMC, E466), methyl cellulose (MC, E461), hydroxypropyl methyl cellulose (HPMC, E464), and hydroxyethyl cellulose (HEC) as sole carbohydrate sources. However, remarkably, collateral metabolism of cellulose ethers was observed when bacteria were primed with low levels of cereal MLG or dicot XyG, in a species-dependent, strain-dependent, and polysaccharide-dependent manner. Using the type strain <i>Segatella copri</i> DSM18205 as an example, cellulose derivative utilization was rationalized by demonstrating that outer membrane-localized <i>endo</i>-glucanases were both transcriptionally upregulated and possessed side activities toward CMC, MC, HPMC, and/or HEC. On one hand, our results <i>in vitro</i> counter the conventional wisdom that soluble cellulose derivatives are non-metabolizable in the human gut. On the other hand, our study suggests that broader analysis of this underappreciated metabolic ability is warranted in a wider range of taxa, especially in consideration of potential physiological effects in the context of balanced diets comprising plant polysaccharides.IMPORTANCEOur data reveal a previously unknown potential among members of the human gut microbiota to metabolize artificial cellulose derivatives used in processed food and oral pharmaceuticals, which is driven by plant glycans ubiquitous in well-balanced diets containing natural dietary fiber. These results challenge the conventional wisdom that cellulose ethers are not broken down and metabolized in monogastric animals and motivate broader exploration of this phenomenon across the numerous autochthonous taxa.</p>","PeriodicalId":15107,"journal":{"name":"Journal of Bacteriology","volume":" ","pages":"e0019825"},"PeriodicalIF":3.0,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144674886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}